dc.contributorFederal University of Alagoas
dc.contributorUniversidade Federal de Pernambuco (UFPE)
dc.contributorScience and Technology of Bahia
dc.contributorEmpresa Brasileira de Pesquisa Agropecuária (EMBRAPA)
dc.contributorUniversidade Estadual Paulista (UNESP)
dc.contributorMax Planck Institute for Plant Breeding Research
dc.date.accessioned2022-04-29T08:35:00Z
dc.date.accessioned2022-12-20T02:54:01Z
dc.date.available2022-04-29T08:35:00Z
dc.date.available2022-12-20T02:54:01Z
dc.date.created2022-04-29T08:35:00Z
dc.date.issued2021-09-23
dc.identifierFrontiers in Genetics, v. 12.
dc.identifier1664-8021
dc.identifierhttp://hdl.handle.net/11449/229659
dc.identifier10.3389/fgene.2021.727314
dc.identifier2-s2.0-85116526697
dc.identifier.urihttps://repositorioslatinoamericanos.uchile.cl/handle/2250/5409793
dc.description.abstractAllopolyploidy is widely present across plant lineages. Though estimating the correct phylogenetic relationships and origin of allopolyploids may sometimes become a hard task. In the genus Stylosanthes Sw. (Leguminosae), an important legume crop, allopolyploidy is a key speciation force. This makes difficult adequate species recognition and breeding efforts on the genus. Based on comparative analysis of nine high-throughput sequencing (HTS) samples, including three allopolyploids (S. capitata Vogel cv. “Campo Grande,” S. capitata “RS024” and S. scabra Vogel) and six diploids (S. hamata Taub, S. viscosa (L.) Sw., S. macrocephala M. B. Ferreira and Sousa Costa, S. guianensis (Aubl.) Sw., S. pilosa M. B. Ferreira and Sousa Costa and S. seabrana B. L. Maass & 't Mannetje) we provide a working pipeline to identify organelle and nuclear genome signatures that allowed us to trace the origin and parental genome recognition of allopolyploids. First, organelle genomes were de novo assembled and used to identify maternal genome donors by alignment-based phylogenies and synteny analysis. Second, nuclear-derived reads were subjected to repetitive DNA identification with RepeatExplorer2. Identified repeats were compared based on abundance and presence on diploids in relation to allopolyploids by comparative repeat analysis. Third, reads were extracted and grouped based on the following groups: chloroplast, mitochondrial, satellite DNA, ribosomal DNA, repeat clustered- and total genomic reads. These sets of reads were then subjected to alignment and assembly free phylogenetic analyses and were compared to classical alignment-based phylogenetic methods. Comparative analysis of shared and unique satellite repeats also allowed the tracing of allopolyploid origin in Stylosanthes, especially those with high abundance such as the StyloSat1 in the Scabra complex. This satellite was in situ mapped in the proximal region of the chromosomes and made it possible to identify its previously proposed parents. Hence, with simple genome skimming data we were able to provide evidence for the recognition of parental genomes and understand genome evolution of two Stylosanthes allopolyploids.
dc.languageeng
dc.relationFrontiers in Genetics
dc.sourceScopus
dc.subjectalignment and assembly free
dc.subjectallopolyploidy
dc.subjectchloroplast
dc.subjectmitochondrion
dc.subjectorganelle genome
dc.subjectrepetitive DNA
dc.subjectsytlosanthes
dc.titleHigh-Throughput Genomic Data Reveal Complex Phylogenetic Relationships in Stylosanthes Sw (Leguminosae)
dc.typeArtículos de revistas


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